Project name: 1A5R_Valen_d

Status: done

Started: 2020-02-17 14:25:32
Settings
Chain sequence(s) A: GSMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:42)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:17:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:17:26)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:17:26)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:17:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:17:31)
[INFO]       Movie:    Creting movie with webm format                                              (00:19:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:05)
Show buried residues
Minimal score value
-4.1372
Maximal score value
0.8488
Average score
-1.3024
Total score value
-134.1465
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
-1 G A -0.9995
0 S A -0.9296
1 M A 0.0000
2 S A 0.0000
3 D A -2.0689
4 Q A -2.6977
5 E A -2.9069
6 A A -1.9685
7 K A -2.0378
8 P A -1.4076
9 S A -1.3131
10 T A -1.3475
11 E A -1.8534
12 D A -1.9143
13 L A 0.0000
14 G A -2.1772
15 D A -2.8218
16 K A -3.3514
17 K A -3.6290
18 E A -3.4839
19 G A -2.4764
20 E A -3.0331
21 Y A -2.6812
22 I A 0.0000
23 K A -3.6499
24 L A 0.0000
25 K A -1.0505
26 V A 0.0000
27 I A 0.3246
28 G A 0.0000
29 Q A -1.8800
30 D A -2.1004
31 S A -1.0041
32 S A -1.2026
33 E A -1.3898
34 I A 0.3428
35 H A -0.7865
36 F A -0.7693
37 K A -2.7960
38 V A 0.0000
39 K A -3.1495
40 M A 0.0000
41 T A -1.8882
42 T A -1.5830
43 H A 0.0000
44 L A 0.0000
45 K A -1.4372
46 K A -1.7813
47 L A 0.0000
48 K A 0.0000
49 E A -1.8759
50 S A -1.6740
51 Y A 0.0000
52 C A 0.0000
53 Q A -2.5582
54 R A -2.5294
55 Q A -1.2362
56 G A -0.9101
57 V A -0.7092
58 P A -0.9289
59 M A -0.8191
60 N A -1.2810
61 S A 0.0000
62 L A 0.0000
63 R A -0.9113
64 F A 0.0000
65 L A -0.6051
66 F A -1.2863
67 E A -2.3136
68 G A -1.8152
69 Q A 0.0000
70 R A -2.0489
71 I A 0.0000
72 A A 0.0000
73 D A 0.0000
74 N A -2.2667
75 H A -2.4218
76 T A 0.0000
77 P A -2.1459
78 K A 0.0000
79 E A -2.6903
80 L A -2.0601
81 G A -1.8681
82 M A 0.0000
83 E A -3.9656
84 E A -4.1372
85 E A -3.9320
86 D A 0.0000
87 V A -0.7753
88 I A 0.0000
89 E A -0.6959
90 V A 0.0000
91 Y A 0.1584
92 Q A -1.0452
93 E A -1.9372
94 Q A -1.9939
95 T A -1.7752
96 G A -1.5004
97 G A -1.5945
98 H A -2.1973
99 S A -1.3284
100 T A -0.4206
101 V A 0.8488
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Play the video

CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -1.3024 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
model_4 -1.3024 View CSV PDB
model_8 -1.3737 View CSV PDB
model_6 -1.377 View CSV PDB
model_0 -1.4554 View CSV PDB
model_10 -1.4574 View CSV PDB
model_9 -1.5403 View CSV PDB
model_3 -1.561 View CSV PDB
model_2 -1.5636 View CSV PDB
model_5 -1.617 View CSV PDB
model_1 -1.6187 View CSV PDB
model_7 -1.6513 View CSV PDB
input -1.6967 View CSV PDB
model_11 -1.7821 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018